===============================================================================
                            1. Receptor Preparation
===============================================================================

This part shows how to prepare an input file for receptor pocket with
'prepare_receptor.py' in 'scripts' directory.

Three files are required (file names in this directory is shown between []):
Receptor PDB: PDB format of receptor structure
	      [rec.pdb]
Ligand PDB: PL-PatchSurfer2 defines receptor pocket by ray-casting method from
       	    co-crystalized ligand. It should be in PDB format
	    [xtal-lig.pdb]
Input file: contains input parameters
      	    [rec_prep.in]

===============================================================================
                    Description of parameters in input file
===============================================================================

PLPS_path: path of PL-PatchSurfer2 package
PDB2PQR_path: path of PDB2PQR is installed
APBS_path: path of APBS is installed
BABEL_path: path of openbabel is installed
receptor_file: receptor PDB file name
ligand_file: ligand PDB file name that is co-crystallized

===============================================================================
                                Runnung Scripts
===============================================================================

Type in command window as below:
$python ../../scripts/prepare_receptor.py rec_prep.in

===============================================================================
                                  Output file
===============================================================================

The output file of the script is SSIC format that contains three-dimensional
Zernike descriptors of all pocket patches

===============================================================================
                           Visualizing seed position
===============================================================================

To see the seed position (center of patch) with molecule structure, generate
PDB file by using 'convert_ssic_to_pdb.py' as below:
$python ../../scripts/convert_ssic_to_pdb.py [SSIC file] [output PDB file]

===============================================================================
